[ADAM-423] Sanitize Avro strings when converting back to SAM.
[ADAM-424] Fix attempts to realign indels when there is no consensus.
[ADAM-425] Skip realignment if no targets are found.
[ADAM-426] Add ability to override indel realigner defaults.
Merge pull request #427 from fnothaft/indel-realigner-errors

Fixes for indel realigner issues
[ADAM-429] adam-submit now handles args correctly.

Makes use of the `gatherSparkSubmitOpts` in Spark's `bin/utils.sh`. Fixes #429
Merge pull request #430 from laserson/ADAM-429

[ADAM-429] adam-submit now handles args correctly.
[ADAM-431] Several random cleanups:

- README tweak

- wrap some long lines

- clarify command parsing in ADAMMain

- quote bash var

- make `GenomicRegionPartitioner` a case class

  seems like it’s well-suited to be one:
  - public ctor vals
  - boilerplate .equals method
  - wrapper ctor that uses companion object method can go into companion
    object

- remove no-op `remapContig` function

  the “NB” comment about it being a no-op seems to be correct, afaict
Merge pull request #431 from ryan-williams/tweaks

[ADAM-431] Several random tweaks:
[ADAM-403] Remove seqDict from RegionJoin

Fixes #403.
Merge pull request #435 from laserson/ADAM-403

[ADAM-403] Remove seqDict from RegionJoin
Adding CountReads object and ReadCounter CLI option.
Adding hasReferenceRegion to ReferenceMapping
[ADAM-420] Adding a package for custom exceptions.

Including UnmappedException as the first (typed) custom exception.

This is so we can include/report better error messages from within ADAM
processes.
[ADAM-297] RegionJoin filters for mappability

There are two changes here:

1. RegionJoin.partitionAndJoin now pre-filters all records on either
side of the join with a check that the records are mappable, and doesn't
try to join those that aren't.

2. RegionJoin attempts to catch the NPE that comes from having
non-mappable records sneak through, and throws an UnmappedException
instead.